The recent creation of bacterial artificial chromosome (BAC) libraries will allow us to sequence and compare portions of sex chromosomes among reptiles and birds. Sex-determining (SD) genes have been found on sex chromosomes in some species and on autosomes in other species. Identification of SD genes consistently found in synteny on either sex chromosomes or autosomes could explain the initiation of sex differentiation in environmentally and genetically SD species. For example, the Sry gene on the Y chromosome initiates sex differentiation in mammals. No Sry homolog has been found in non-mammalian vertebrates. We will use flourescent in situ hybridization and chromosome painting to locate SD genes in representative reptiles and birds. We will compare syntenies of SD genes. Our mapping of SD genes and syntenies will be compared with patterns of heterogamety and SD mechanism. Our broad approach to comparative genomics will allow us to address questions about initiation of sex differentiation in birds and reptiles, genomic differences between species with either genetic or environmental SD mechanisms, causes of chromosomal degeneration, and the history of heteromorphic chromosomes in birds and reptiles.